Linux shell crash course¶
This is a kickstart for the Linux shell, to teach the minimum amount needed for any scientific computing course. For more, see the linux shell course or the references below.
This is basic B-level: no prerequisites.
Watch this in video format
There is a companion video on YouTube, if you would also like that format.
If you are reading this case, you probably need to do some sort of scientific computing involving the Linux shell, or command line interface. You may wonder why we are still using a command line today, but the answer is somewhat simple: once you are doing scientific computing, you eventually need to script and automate something. The shell is the only method that gives you the power to do anything you may want.
These days, you don’t need to know as much about the shell as you used to, but you do need to know a few important commands because the command line works when nothing else does - and you can’t do scripting without it.
What’s a shell?¶
It’s the old-fashioned looking thing where you type commands with a keyboard and get output to the screen. It seems boring, but the real power is that you can script (program) commands to run automatically - which is the point of scientific computing.
You type a command, which may include arguments. Output gets
shown to the screen. Spaces separate commands and arguments.
cp -i file1.txt file2.txt. cp is the command, -i is
an option, file1.txt and file2.txt are arguments.
Files are represented by filenames, like
Directories are separated by
/, for example
is file.txt inside of mydir.
Exercise: Start a shell. On Linux or Mac, the “terminal” application does this.
Editing and viewing files¶
nano is an editor which allows you to edit files directly
from the shell. This is a simple console editor which always gets the
job done. Use Control-x (control and x at the same time), then
y when requested and enter, to save and exit.
less is a pager (file viewer) which lets you view files
without editing them. (
q to quit,
/ to search,
to research forward and backwards,
< for beginning of file,
for end of file)
Listing and moving files¶
ls lists the current directory.
ls -l shows more
ls -a shows hidden files. The options can be
ls -la or
ls -l -a. This pattern of options is
standard for most commands.
mv will move or rename files. For example,
cp will make a copy of a file, with the exact same syntax as
cp file.old file.copy.
rm will remove a file:
rm file.txt. To remove a directory,
rm -r. Note that
rm does not have backups and does not
ask for confirmation!
mkdir makes a directory:
Unlike with a graphical file browser, there is a concept of current
working directory: each shell is in a current directory. If you
ls, it lists files in your current directory. If a program tries
to open a file, it opens it relative to that directory.
cd dirname will change working directories for your current
shell. Normally, you will
cd to a working directory, and use
relative paths from there.
/ alone refers to the root
directory, the parent of all files and directories.
cd .. will change to the parent directory (dir containing this
dir). By the same token,
../.. the parent of the parent, and so
Exercise: Change to some directory and then another. What do
cd -) and (
cd with no arguments) do? Try each a few times in
Online manuals for any command¶
man is an on-line manual, type
man ls to get help on the
ls command. The same works for almost any program. Some are easy
to read, some are impossible. In general you look for what you need,
not read everything. Use
q to quit or
/ to search (
N to search again forward and backwards).
-h is a standard argument that prints a short
Exercise: briefly look at the manual pages and
for the commands we have learned thus far. How can you make
ask before removing a file?
History and tab completion¶
Annoyed at typing so much? We’ve got two ways to make work faster.
First, each shell keeps its (shell) history. By pushing the up arrow key, you can access previous lines. Never type similar things twice, go up in history and find the previous line, modify it, then push enter to re-run.
Shells also have tab completion. Type the first few letters of any command or filename and push tab once or twice… it will either complete it or show you the options. This is so important that it’s used often, and many command arguments can also be completed.
Exercise: Play around with tab completion. Type
TAB. (erase that then start over) Then type
p and push
TAB twice. (erase that and start over) Then
ls, space, and
the first few letters of a filename, then push
- The linux shell course has much more detail.
- Software Carpentry has a basic shell course. Sections one to 3 are details of what is above (the rest is about shell scripting).
Exercise: for some fun, look at the manual pages for
Exercise (advanced): read the Linux shell course and understand what “pipes” and “piping” are.